Preheat oven to 375 degrees. Add first 10 ingredients to a Dutch oven or oven safe pot. Place thyme sprigs on top of ingredients and place Dutch oven with top on into your preheated oven. Cook for 1 hour and 15 minutes, then remove top and cook for an additional 30 minutes. Remove the pot from the oven and add the chicken stock, heavy cream, flour and butter. Simmer on the stove on medium heat for 15 minutes. Add 1 Granny Smith apple diced to garnish the soup.